Downwelling vector irradiance as photons of electromagnetic radiation (PAR wavelengths) in the water body by cosine-collector radiometer

OXYSSC01

1

Percent

BK_SBE43

Saturation of oxygen {O2 CAS 7782-44-7} in the water body [dissolved plus reactive particulate phase] by Sea-Bird SBE 43 sensor and calibration against sample data and computation from concentration using Benson and Krause algorithm

POPTZZ01

1

Percent

Trans_Unspec

Transmittance (unspecified wavelength) per unspecified length of the water body by transmissometer

POTMCV01

1

Degrees Celsius

WC_Potemp

Potential temperature of the water body by computation using UNESCO 1983 algorithm

PRESPR01

1

Decibars

Pres_Z

Pressure (spatial co-ordinate) exerted by the water body by profiling pressure sensor and corrected to read zero at sea level

PSALCC01

1

Dimensionless

P_sal_CTD_calib

Practical salinity of the water body by CTD and computation using UNESCO 1983 algorithm and calibration against independent measurements

SIGTPR01

1

Kilograms per cubic metre

SigTheta

Sigma-theta of the water body by CTD and computation from salinity and potential temperature using UNESCO algorithm

TEMPCU01

1

Degrees Celsius

Uncal_CTD_Temp

Temperature of the water body by CTD and NO verification against independent measurements

Definition of Rank

Rank 1 is a one-dimensional parameter

Rank 2 is a two-dimensional parameter

Rank 0 is a one-dimensional parameter describing the second dimension of a two-dimensional parameter (e.g. bin depths for moored ADCP data)

Open Data supplied by Natural Environment Research Council (NERC)

Sea-Bird Dissolved Oxygen Sensor SBE 43 and SBE 43F

The SBE 43 is a dissolved oxygen sensor designed for marine applications. It incorporates a high-performance Clark polarographic membrane with a pump that continuously plumbs water through it, preventing algal growth and the development of anoxic conditions when the sensor is taking measurements.

Two configurations are available: SBE 43 produces a voltage output and can be incorporated with any Sea-Bird CTD that accepts input from a 0-5 volt auxiliary sensor, while the SBE 43F produces a frequency output and can be integrated with an SBE 52-MP (Moored Profiler CTD) or used for OEM applications. The specifications below are common to both.

James Clarke Ross Cruise JR218 JCR20081003 AMT18 CTD Instrumentation

The CTD unit was a Sea-Bird Electronics 911 plus system, with dissolved oxygen sensor. The CTD was fitted with a transmissometer, a fluorometer and PAR sensor. All instruments were attached to a Sea-Bird SBE 32 carousel. The table below lists more detailed information about the various sensors.

Sensor

Model

Serial Number

Calibration

Comments

Pressure transducer

Digiquartz temperature compensated pressure sensor

0541-75429

18/07/2007

-

Conductivity sensor 1

SBE 4C

2875

18/07/2007

-

Conductivity sensor 2

SBE 4C

n/a

n/a

-

Temperature sensor 1

SBE 3P

4302

18/07/2007

-

Temperature sensor 2

SBE 3P

4235

18/07/2007

-

Dissolved oxygen

SBE 43

0676

26/07/2007

-

Transmissometer

Wetlabs C-Star 6000m

CST-527DR

14/08/2007

0.25 m path

Fluorometer

Chelsea MkIII Aquatracka

088-249

13/09/2007

-

PAR Sensor

Biospherical Instruments QCD

72350

26/07/2007

-

Change of sensors during cruise: None reported.

Sampling device

Sea-Bird Electronics SBE 911 and SBE 917 series CTD profilers

The SBE 911 and SBE 917 series of conductivity-temperature-depth (CTD) units are used to collect hydrographic profiles, including temperature, conductivity and pressure as standard. Each profiler consists of an underwater unit and deck unit or SEARAM. Auxiliary sensors, such as fluorometers, dissolved oxygen sensors and transmissometers, and carousel water samplers are commonly added to the underwater unit.

Underwater unit

The CTD underwater unit (SBE 9 or SBE 9 plus ) comprises a protective cage (usually with a carousel water sampler), including a main pressure housing containing power supplies, acquisition electronics, telemetry circuitry, and a suite of modular sensors. The original SBE 9 incorporated Sea-Bird's standard modular SBE 3 temperature sensor and SBE 4 conductivity sensor, and a Paroscientific Digiquartz pressure sensor. The conductivity cell was connected to a pump-fed plastic tubing circuit that could include auxiliary sensors. Each SBE 9 unit was custom built to individual specification. The SBE 9 was replaced in 1997 by an off-the-shelf version, termed the SBE 9 plus , that incorporated the SBE 3 plus (or SBE 3P) temperature sensor, SBE 4C conductivity sensor and a Paroscientific Digiquartz pressure sensor. Sensors could be connected to a pump-fed plastic tubing circuit or stand-alone.

Temperature, conductivity and pressure sensors

The conductivity, temperature, and pressure sensors supplied with Sea-Bird CTD systems have outputs in the form of variable frequencies, which are measured using high-speed parallel counters. The resulting count totals are converted to numeric representations of the original frequencies, which bear a direct relationship to temperature, conductivity or pressure. Sampling frequencies for these sensors are typically set at 24 Hz.

The temperature sensing element is a glass-coated thermistor bead, pressure-protected inside a stainless steel tube, while the conductivity sensing element is a cylindrical, flow-through, borosilicate glass cell with three internal platinum electrodes. Thermistor resistance or conductivity cell resistance, respectively, is the controlling element in an optimized Wien Bridge oscillator circuit, which produces a frequency output that can be converted to a temperature or conductivity reading. These sensors are available with depth ratings of 6800 m (aluminium housing) or 10500 m (titanium housing). The Paroscientific Digiquartz pressure sensor comprises a quartz crystal resonator that responds to pressure-induced stress, and temperature is measured for thermal compensation of the calculated pressure.

Additional sensors

Optional sensors for dissolved oxygen, pH, light transmission, fluorescence and others do not require the very high levels of resolution needed in the primary CTD channels, nor do these sensors generally offer variable frequency outputs. Accordingly, signals from the auxiliary sensors are acquired using a conventional voltage-input multiplexed A/D converter (optional). Some Sea-Bird CTDs use a strain gauge pressure sensor (Senso-Metrics) in which case their pressure output data is in the same form as that from the auxiliary sensors as described above.

Deck unit or SEARAM

Each underwater unit is connected to a power supply and data logging system: the SBE 11 (or SBE 11 plus ) deck unit allows real-time interfacing between the deck and the underwater unit via a conductive wire, while the submersible SBE 17 (or SBE 17 plus ) SEARAM plugs directly into the underwater unit and data are downloaded on recovery of the CTD. The combination of SBE 9 and SBE 17 or SBE 11 are termed SBE 917 or SBE 911, respectively, while the combinations of SBE 9 plus and SBE 17 plus or SBE 11 plus are termed SBE 917 plus or SBE 911 plus .

Chelsea Technologies Group Aquatracka MKIII fluorometer

The Chelsea Technologies Group Aquatracka MKIII is a logarithmic response fluorometer. Filters are available to enable the instrument to measure chlorophyll, rhodamine, fluorescein and turbidity.

It uses a pulsed (5.5 Hz) xenon light source discharging along two signal paths to eliminate variations in the flashlamp intensity. The reference path measures the intensity of the light source whilst the signal path measures the intensity of the light emitted from the specimen under test. The reference signal and the emitted light signals are then applied to a ratiometric circuit. In this circuit, the ratio of returned signal to reference signal is computed and scaled logarithmically to achieve a wide dynamic range. The logarithmic conversion accuracy is maintained at better than one percent of the reading over the full output range of the instrument.

Two variants of the instrument are available, both manufactured in titanium, capable of operating in depths from shallow water down to 2000 m and 6000 m respectively. The optical characteristics of the instrument in its different detection modes are visible below:

Excitation

Chlorophyll a

Rhodamine

Fluorescein

Turbidity

Wavelength (nm)

430

500

485

440 *

Bandwidth (nm)

105

70

22

80 *

Emission

Chlorophyll a

Rhodamine

Fluorescein

Turbidity

Wavelength (nm)

685

590

530

440 *

Bandwidth (nm)

30

45

30

80 *

* The wavelengths for the turbidity filters are customer selectable but must be in the range 400 to 700 nm. The same wavelength is used in the excitation path and the emission path.

The instrument measures chlorophyll a, rhodamine and fluorescein with a concentration range of 0.01 µg l -1 to 100 µg l -1 . The concentration range for turbidity is 0.01 to 100 FTU (other wavelengths are available on request).

The instrument accuracy is ± 0.02 µg l -1 (or ± 3% of the reading, whichever is greater) for chlorophyll a, rhodamine and fluorescein. The accuracy for turbidity, over a 0 - 10 FTU range, is ± 0.02 FTU (or ± 3% of the reading, whichever is greater).

The QCD-905L is a submersible radiometer designed to measure irradiance over Photosynthetically Active Radiation (PAR) wavelengths (400-700 nm). It features a cosine directional response when fully immersed in water.

The sensor is a blue-enhanced high stability silicon photovoltaic detector with dielectric and absorbing glass filter assembly, and produces a logarithmic output. Normal output range is -1 to 6 volts with 1 volt per decade. Typically, the instrument outputs 5 volts for full sunlight and has a minimum output of 0.001% full sunlight, where typical noon solar irradiance is 1.5 to 2 x 10 17 quanta cm -2 s -1 . The instrument can be calibrated with constants for µE cm -2 s -1 or quanta cm -2 s -1 .

The QCD-905L can be coupled to a fixed range data acquisition system like a CTD (Conductivity-Temperature-Depth) profiler or current meter. It has an aluminium and PET housing, and a depth rating of 7000 m.

Specifications

Paroscientific Absolute Pressure Transducers Series 3000 and 4000

Paroscientific Series 3000 and 4000 pressure transducers use a Digiquartz pressure sensor to provide high accuracy and precision data. The sensor comprises a quartz crystal resonator that responds to pressure-induced stress, and temperature is measured for thermal compensation of the calculated pressure.

The 3000 series of transducers includes one model, the 31K-101, whereas the 4000 series includes several models, listed in the table below. All transducers exhibit repeatability of better than ±0.01% full pressure scale, hysteresis of better than ±0.02% full scale and acceleration sensitivity of ±0.008% full scale /g (three axis average). Pressure resolution is better than 0.0001% and accuracy is typically 0.01% over a broad range of temperatures.

Differences between the models lie in their pressure and operating temperature ranges, as detailed below:

WETLabs C-Star transmissometer

This instrument is designed to measure beam transmittance by submersion or with an optional flow tube for pumped applications. It can be used in profiles, moorings or as part of an underway system.

Two models are available, a 25 cm pathlength, which can be built in aluminum or co-polymer, and a 10 cm pathlength with a plastic housing. Both have an analog output, but a digital model is also available.

This instrument has been updated to provide a high resolution RS232 data output, while maintaining the same design and characteristics.

James Clark Ross Cruise JR218 JR20081003 AMT18 CTD Processing

Sampling strategy

A total of 102 successful CTD casts were made during the cruise. However, the logging software crashed during two casts (CTD083 and CTD093) and the split files were not processed on board. Rosette bottles were fired throughout the water column on the upcast of most profiles. Data were measured at 24 Hz by a PC running SEASAVE, Sea-Bird's data acquisition software. The processed profiles were supplied to BODC after the cruise

Originator's processing

CTD casts were recorded using the SeaBird data collection software Seasave-Win32. The software outputs were then processed using SBE Data Processing-Win32 v7.18; the processing routines are named after each stage in brackets. The software applied the calibrations as appropriate through the instrument configuration file to the data in engineering units output by the CTD hardware. A binary file including the 24 Hz data for up and down casts was generated along with a bottle file containing all the information from the instant the bottle was fired for each cast (DatCnv). The oxygen sensor was then shifted relative to the pressure by 5 seconds, to compensate for the lag in the sensor response time (AlignCTD). Pressure spikes were removed (WildEdit), the effect of thermal 'inertia' on the conductivity cells was removed (CellTM) and then the binary files were converted to ascii so they could be read in PSTAR format (translate).

The CTD files produced from SeaBird processing were converted from 24 Hz ascii files into PSTAR format (ctd0). The data were than averaged into a 1 Hz file. A file was created for each cast containing the mean values of all the variables at the bottle firing locations. Bench salinometer data were collected during the cruise from a range of depths from each CTD cast. The salinometer data was compared with CTD values from the primary and secondary sensor during processing by NOC's staff on the cruise and a calibration applied. Details of these calibrations are given in the Underway Physics report and post cruise addendum in the Cruise Report.

BODC post-processing and screening

Sea-Bird processing

No further processing was carried out by BODC.

Reformatting

The data were converted from PSTAR binary format into BODC internal format (QXF) using BODC transfer function 360. The following table shows how the variables within the PSTAR files were mapped to appropriate BODC parameter codes:

Originator's Parameter Name

Units

Description

BODC Parameter Code

Units

Comments

Pressure, Digiquartz

dbar

CTD pressure

PRESPR01

dbar

-

temp

°C

Temperature of water column by CTD

TEMPCU01

°C

-

temp2

°C

Temperature of water column by CTD

TEMPCU02

°C

-

salin

-

Practical salinity of the water body by CTD

PSALCC01

-

Calibrated against bench salinometer samples by origintors

salin2

-

Practical salinity of the water body by CTD

PSALCC02

-

Calibrated against bench salinometer samples by origintors

oxygen

ml l -1

Dissolved oxygen concentration

DOXYSU01

µmol l -1

Converted from ml l -1 to µmol l -1 by multiplying the original value by 44.66.

fluor

mg m -3

Fluorometer nominal chlorophyll-a

CPHLPM01

mg m -3

-

PAR irradiance

µE m -2 s -1

Downwelling PAR irradiance

IRRDUV01

µE m -2 s -1

-

Atten

m -1

Beam attenuance

ATTNZZ01

m -1

25cm pathlength

-

-

Oxygen

DOXYSC01

µmol l -1

BODC calibration of DOXYSU01 against Winkler samples

-

-

Chlorophyll-a

CPHLPS01

mg m -3

BODC calibration of CPHLPM01 against HPLC pigment samples

-

-

Oxygen saturation

OXYSSC01

%

Generated by BODC using the Benson and Krause (1984) algorithm with parameters DOXYSC01, PSALCC01 and TEMPCU01

UNESCO, 1981. Background papers and supporting data on the International Equation of State of Seawater 1980. UNESCO Technical Papers in Marine Science No. 38, 192pp

Screening

Reformatted CTD data were transferred onto a graphics work station for visualisation using the in-house editor EDSERPLO. Downcasts and upcasts were differentiated and the limits manually flagged. No data values were edited or deleted. Flagging was achieved by modification of the associated BODC quality control flag for suspect or null values.

From visual screening of the 1 Hz data profiles, it was clear that the profiles suffered from the problem of ship's heave/entrainment, which has now become conspicuous on most cruises. Records from the primary and secondary sensors are almost identical suggesting that the two sensors were located in close proximity. Significant entrainment anomalies on the primary channels were flagged systematically whenever it was believed that they would affect the quality of the 1 dbar-binned data. Since data from the secondary channels were almost identical to those from the primary sensors they can be used as a reference for what the profile, once averaged into 1 dbar bins, would be like had the anomalies not been flagged.

Screening notes regarding specific casts:

CTD casts 001, 068, 073, 077 and 081 were shallow casts to ~20m depth. It did not appear that the CTD rig was soaked before these casts and the data was very noisy for the first 10 m of the downcast profile. The upcast data on the other hand appeared of better quality. In these situations a decision was taken to quality control, then bank the data from the upcast.

Users should be aware that CTD cast 010 has a large amount of variability recorded for all parameters in the depth range 50-80m. Over this range the CTD rig appeared to be rotating as it descended, resulting in a corkscrew profile down through the water column. This was not flagged as it would have removed a large portion of the data collected for this depth range.

Salinity: CTD casts 044 and 045 have a salinity minimum at the surface which was considered suspect at first but left unflagged because of its presence in two consecutive profiles and because there was also some evidence of near-surface stratification on the upcast.

Dissolved oxygen: CTD casts 001 to 017, flags were applied to loops and bottom drift which were skewing good data. After that the profiles were better and the loops generally small enough to be ignored. On some casts (e.g. cast 043) large anomalies were seen but no flags were applied because of the difficulty in identifying good from bad data points.

Fluorescence: The profiles were generally good without too much noise even at low concentration. The problem related to water entrainment was mainly observed in the more productive waters where fluorescence gradients were sharper. Casts 099-102 in particular suffered from large anomalies associated with entrainment features on the lower part of the chlorophyll maximum. Again, the difficulty in identifying good from bad data meant that these features were not flagged.

Beam attenuance and transmissance: For the transmittance channel users should be aware that the CTD029 profile data were very noisy below 900 dbar but have not been flagged. As with the fluorescence casts 99-102 have some unflagged features related to water entrainment. The WetLabs C-star transmissometer profiles did not display the hysteresis coincident with high temperature gradients observed in previous AMT cruises that deployed Chelsea Alphatracka transmissometers.

Downwelling PAR: Spiky data were generally associated with movement when the package was going down too slowly and "bouncing" in the surface layer. However the majority of casts were not flagged given that the variation can be the result of variation in surface conditions (e.g. changing cloud cover). Some low PAR spikes were believed to be associated with ship shading and were flagged suspect on casts 023, 036, 053, 054 and 092.

Banking

Once quality control screening was complete, the CTD downcasts were banked. Finally, the data were binned against pressure at 1 dbar increments and data flagged suspect were not included in these bin calculations. The primary salinity, temperature, density and potential temperature channels were selects as the best quality profiles for banking in the database.

Field Calibrations

Pressure

There were no casts where the CTD pressure was logging in air. No adjustments were made to the values resulting from application of manufacturer's coefficients during the initial processing.

Temperature

Temperature readings from the two temperature sensors were almost identical and no other independent measurements of better quality were available. No further correction was therefore applied to the data.

Salinity

The salinity channels have been calibrated by the originators and no further correction was applied to the data.

Dissolved oxygen

The oxygen sensors were calibrated using the sensor readings from the upcast at the point when the bottles were fired and the dissolved oxygen data measured using the Winkler titration methodology on water samples collected from bottles. The samples collected were from a range of depths on a number of casts throughout the cruise. The major outliers from the calibration related to samples collected from depths greater than 1000m. Users should be aware that the SBE 43 oxygen sensor is documented by SeaBird as having a potential problem with hysteresis at pressures greater than 1000 db and the calibration will not be as accurate beyond this depth for some casts.

Casts

Calibration

N

R 2

BODC cal ref

All

DOXYSC01 = 1.2299 * DOXYSU01 + 3.5301

67

0.992

6442

Fluorescence

The nominal chlorophyll-a values were calculated from the fluorometer data (with manufacturer's calibration applied) from the up-cast at bottle firing and the HPLC chlorophyll-a data from sampled bottles. The calibration dataset did not have data from all casts and with some CTDs only having 1 sample with HPLC pigment data provided and where this data appeared to be an outlier the cast could not be reliably calibrated. Therefore casts 1-3, 9-10 and 101-102 were not calibrated. The remaining casts were split into 2 groups and regressions were significant (p<0.001).

The Atlantic Meridional Transect has been operational since 1995 and through the Oceans 2025 programme secures funding for a further five cruises during the period 2007-2012. The AMT programme began in 1995 utilising the passage of the RRS James Clark Ross between the UK and the Falkland Islands southwards in September and northwards in April each year. Prior to Oceans 2025 the AMT programme has completed 18 cruises following this transect in the Atlantic Ocean. This sustained observing system aims to provide basin-scale understanding of the distribution of planktonic communities, their nutrient turnover and biogenic export in the context of hydrographic and biogeochemical provinces of the North and South Atlantic Oceans.

The Atlantic Meridional Transect Programme is an open ocean in situ observing system that will:

give early warning of any fundamental change in Atlantic ecosystem functionng

improve forecasts of the future ocean state and associated socio-economic impacts

provide a "contextual" logistical and scientific infrastructure for independently-funded national and international open ocean biogeochemical and ecological research.

The specific objectives are:

To collect hydrographic, chemical, ecological and optical data on transects between the UK and the Falkland Islands

To quantify the nature and causes of ecological and biogeochemical variability in planktonic ecosystems

To assess the effects of variability in planktonic ecosystems on biogenic export and on air-sea exchange of radiatively active gases

The measurements taken and experiments carried out on the AMT cruises will be closely linked to Themes 2 and 5. The planned cruise track also allows for the AMT data to be used in providing spatial context to the Sustained Observation Activities at the Porcupine Abyssal Plain Ocean Observatory (SO2) and the Western Channel Observatory (SO10).

More detailed information on this Work Package is available at pages 6 - 9 of the official Oceans 2025 Theme 10 document: Oceans 2025 Theme 10